Bioinformatics Core Facility

Welcome

The Nemours Bioinformatics Core facility (BCF) provides consultation, training and computational resources (both hardware and software) to Nemours Biomedical Research investigators from both Delaware and Florida.

BCF manages the primary web / email / database servers for asel.udel.edu and NemoursResearch.org with 10 computing cores, 16GB of RAM and 5TB of disk space for user accounts. Additional Linux-based research servers provide 108 CPU cores, 462 GB of RAM and 102 TB of RAID disk space for research labs. Up to 32 CPU cores and 256G of memory can be used for traditional parallel computing tasks and a dedicated 8-node 192 core 20TB Apache Spark/Hadoop computing cluster is available for big data related projects. A dedicated backup system provides hourly backups of email, daily disk backups of file volumes, and weekly LTO5 tape backups which are stored off-site.

Services offered by BCF include experimental design of parallel, crossover, longitudinal, cross-section and microarray studies; data mining of microarray and high-throughput sequencing studies; and standard statistical analysis. BCF utilizes many software packages including SPSS, SAS, R, Bioconductor, MeV, CMfinder, MOSAIK and more. With the use of several programming languages (PERL, MySQL, PHP, HTML, Javascript) BCF can also develop custom scripts and applications for studies. BCF has developed and maintains several web applications including TimeKeeper, the Biosafety Database, NED (Nemours Experimental Database, an electronic lab notebook), Symposia registration and SNAP ("Scientist Networking And Profiles" site using Drupal, a web content management system).

BCF also manages the Nemours installation of REDCapTM (Research Electronic Data Capture from the REDCap Consortium). REDCap is a secure web application that allows users to build and manage online surveys and databases for a variety of purposes including basic, clinical, translational and behavioral research, repositories and operational support. In addition to maintaining this application, BCF provides training and other support so that Nemours associates can utilize all the tools this resource provides.

Additional REDCap Info

Here are some reasons you should consider using REDCap instead of spreadsheets for recording research data:

1.) Accessibility - everyone in the lab can get to the data and do data entry from anywhere.

2.) Security - Data is stored on our servers, backed up nightly. Users must authenticate to view it. Users can be assigned different levels of permission such as read-only, add/edit data, delete records, etc. Users can also be restricted from viewing certain forms and exporting certain fields.

3.) Versatility - Data or data subsets can be easily selected, sorted, and exported in formats directly ready for analysis in SPSS, SAS, S+/R, or even Excel. Schedules can be automatically generated from defined events.

4.) Validity - Using a tool like REDCap to set up a database and data entry forms for a study is a valuable first step in being sure that you have covered all the devilish details that are inherent in designing a valid research study. The bioinformatics staff have expertise in database design and biostatistics and can help assure that your study is well thought out and implemented.

To learn more about REDCap, send us an email, or visit the REDCap Training Resources page. (Note that you do not need to log into REDCap to view the tutorial videos).